The historic gold rush era and atmospheric deposition in California have led to mercury (Hg) contamination in surface waters. The organic form of Hg, methylmercury (MeHg), bioaccumulates in the food chain and poses a negative health effect for wildlife and humans consuming contaminated fish, seafood, and rice. Controlling MeHg production is challenging due to its dependency on multiple site-specific and interrelated environmental conditions. In this dissertation, I examined the factors contributing to MeHg production, the methylation window, in two aquatic environments: Hodges Reservoir (a lake-like environment), and Cache Creek Settling Basin, CCSB (a wetland-like environment). Additionally, I explored two mercury remediation techniques, a hypolimnetic oxygenation system (HOS) and coagulation with metal-based salts. In Hodges Reservoir, a hypereutrophic sulfate-rich water supply reservoir located in San Diego, CA, field monitoring revealed that before oxygenation, winter precipitation and changes in hypolimnion volume mechanistically affected the biogeochemistry processes of the reservoir, especially the Hg cycle (Chapter 1). During wet years, a spring methylation window opened as precipitation provided additional mass of oxygen due to a larger hypolimnion. This maintained mildly reduced conditions that enhanced Hg methylation in bottom waters. But during dry years, the methylation window closed earlier in the season because of the development of highly reduced conditions favoring demethylation relative to methylation, and due to the buildup of sulfide concentration decreasing inorganic Hg bioavailability. Following HOS implementation, oxygenation appeared to suppress anaerobic bacteria activity responsible for MeHg production, indicating the potential usefulness of techniques designed to keep bottom lake water oxidized for repressing MeHg production. In CCSB, located in the Sacramento Valley, CA, the United States Geological Survey (USGS) studied the use of the coagulants ChitoVan™ (organic/shell amino-based), Ferralyte® (ferric-sulfate-based), and Ultrion® (polyaluminum chloride-based) to immobilize Hg from Cache Creek into the sediment. Bench-scale sediment-water slurry incubations with CCSB soils from USGS field experiments demonstrated that organic matter is the main driver for MeHg production (Chapter 2). The three different coagulant-treated soils were not a source of MeHg under rewetted conditions (standard test). However, under elevated organic matter loading (stress test), inorganic Hg could be potentially released. In a follow-up experiment using CCSB non-treated soils and water under a gradient of algal organic matter (Spirulina powder), the addition of more than 0.1 g of algal organic matter to 250 ml sediment-water slurries appeared to activate a diverse microbial community that led to an ephemeral window of MeHg production (Chapter 3). Analysis of dissolved organic matter (DOM) optical properties using fluorescence spectroscopy indicated that some regions of the DOM (F, B, and FI index) could correlate to the window of MeHg production. This suggests that monitoring DOM optical characteristics in the field could hold promise in better understanding MeHg production and bioaccumulation in aquatic ecosystems. Overall, the outcomes of these studies indicate that oxygenation and controlling organic matter loading are viable management strategies to mitigate Hg contamination in managed aquatic ecosystems. Note, Appendix includes supplementary material and raw data for Chapters 2 and 3.